China’s northern Hulun Lake is a significant body of water internationally. The issue of eutrophication has gained prominence in recent years. The achievement of precise chlorophyll-a (Chl-a) monitoring is crucial for safeguarding Hulun Lake’s ecosystem. The machine learning-based remote sensing inversion method has been shown to be effective in capturing the intricate relationship between independent and dependent variables; however, it lacks a priori knowledge and is limited by the quality of remote sensing data sources. The relationship between independent and dependent variables can be more accurately simulated with the use of suitable auxiliary variables. Therefore, three machine learning models—random forest (RF), adaptive boosting (AdaBoost), and extreme gradient boosting (XGBoost)—were established in this study using meteorological observation parameters as auxiliary variables combined with Sentinel-2 satellite image remote sensing band combinations as independent variables and measured Chl-a data as dependent variables. The estimation effects before and after the fusion of meteorological ground observation data were compared, and the best model was used to estimate the spatial–temporal variation trend of Chl-a in the regional water body. The results show that (1) the addition of meteorological parameters as auxiliary variables improved the precision of the three machine models; the decision coefficient (R2) rose by 7.25%, 5.71%, and 7.20%, respectively, to 0.76, 0.66, and 0.73. (2) The concentration of Chl-a in the lake region was projected from June to October 2019 to October 2021 using the RF optimal estimating model of meteorological fusion. The northeast, southwest, and south of the lake were where the comparatively high concentration values of Chl-a were located, whereas the lake’s center had a generally low concentration of the substance. Chromatically, Chl-a typically peaked in August after initially increasing and then declining. (3) The three rivers that feed into the river have varying levels of water pollution, with chemical oxygen demand (COD) and total nitrogen (TN) pollution being the most severe. This is what primarily caused the higher levels of Chl-a in the northeast, southwest, and south. This study is crucial for the preservation and restoration of Hulun Lake’s natural ecosystem and offers some technical support for the monitoring of the lake’s concentration of Chl-a.